Contacts of the helix formed by residues 323 - 342 (chain A) in PDB entry 3T2D
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ARG* 3.5 9.5 + - - +
320A LEU 5.7 1.3 - - - +
321A PHE 3.3 2.0 + - - -
322A ASP* 1.3 76.9 - - - +
324A PRO* 1.3 78.5 - - - +
325A ALA* 2.8 35.4 + - - +
326A PHE* 2.9 27.9 + - + +
327A ASP 3.2 6.9 + - - -
330A ARG* 3.5 6.2 + - - -
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Residues in contact with PRO 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ARG* 4.2 2.4 - - - +
323A ASP* 1.3 93.4 - - - +
325A ALA* 1.3 61.0 + - - +
327A ASP* 3.0 34.1 + - + +
328A TYR* 3.5 6.2 + - - +
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Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ASP* 2.8 26.8 + - + +
324A PRO* 1.3 72.7 - - - +
326A PHE* 1.3 64.1 + - + +
328A TYR* 3.6 17.5 + - - +
329A VAL* 3.8 9.8 - - - +
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Residues in contact with PHE 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU* 3.6 31.9 - - + -
253A GLU* 5.5 0.2 - - - -
255A PHE 4.1 1.8 - - - -
256A ALA* 4.0 24.5 - - + -
275A PRO* 3.7 24.5 - - + -
320A LEU 4.1 7.9 - - - -
321A PHE* 3.5 59.7 - + - +
323A ASP* 2.9 13.8 + - + +
325A ALA* 1.3 77.4 - - + +
327A ASP* 1.3 66.4 + - - +
328A TYR 3.2 1.8 - - - -
329A VAL* 3.1 11.7 + - + +
330A ARG* 3.0 32.3 + - - +
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Residues in contact with ASP 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ARG* 2.9 24.5 + - - -
323A ASP 3.2 1.6 + - - -
324A PRO* 3.0 26.9 + - - +
326A PHE* 1.3 77.0 - - - +
328A TYR* 1.3 56.2 + - - +
330A ARG* 2.9 28.9 + - - +
331A GLN* 2.9 48.8 + - - +
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Residues in contact with TYR 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A PRO 3.5 6.3 + - - +
325A ALA* 3.7 11.4 - - - +
326A PHE 3.2 0.4 - - - -
327A ASP* 1.3 79.4 - - - +
329A VAL* 1.3 67.0 + - + +
331A GLN* 3.3 20.1 + - + +
332A THR* 3.0 42.1 + - - -
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Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PHE 4.2 0.2 - - - +
256A ALA* 3.2 37.7 - - + +
258A PRO* 3.8 15.6 - - + +
275A PRO* 3.5 27.8 - - + -
325A ALA 3.8 14.4 - - - +
326A PHE* 3.1 22.8 + - + +
328A TYR* 1.3 83.5 - - + +
330A ARG* 1.3 56.3 + - - +
332A THR* 3.3 8.2 + - - -
333A ALA* 2.9 27.1 + - - +
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Residues in contact with ARG 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A MET* 3.7 30.5 - - + +
275A PRO* 2.8 37.7 + - + +
276A ALA* 4.4 7.9 - - - +
277A ARG* 3.2 32.9 - - - +
321A PHE* 2.9 33.5 + - - +
323A ASP 3.5 1.2 + - - -
326A PHE* 3.0 19.6 + - - +
327A ASP* 2.9 42.0 + - - +
329A VAL* 1.3 76.1 - - - +
331A GLN* 1.3 57.9 + - + +
333A ALA* 3.2 2.6 + - - +
334A ALA* 2.9 29.5 + - - +
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Residues in contact with GLN 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ASP* 2.9 34.5 + - - +
328A TYR* 3.6 25.0 - - + +
329A VAL 3.3 0.2 - - - -
330A ARG* 1.3 72.8 - - + +
332A THR* 1.3 64.6 + - - +
334A ALA* 3.2 8.1 + - - +
335A GLN* 3.0 38.4 + - - +
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Residues in contact with THR 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A HIS* 5.9 3.1 - - + +
258A PRO* 3.9 20.0 - - + -
328A TYR* 3.0 34.3 + - - -
329A VAL* 3.5 10.7 - - - -
331A GLN* 1.3 74.5 - - - +
333A ALA* 1.3 65.1 + - - +
335A GLN* 3.2 13.9 + - - +
336A ILE* 2.9 36.4 + - + +
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PRO* 3.9 20.2 - - + +
272A PRO* 3.3 24.1 - - + +
274A MET* 4.0 29.2 - - + -
299A PRO* 5.6 0.4 - - + -
329A VAL 2.9 14.6 + - - +
330A ARG 3.2 8.0 + - - +
332A THR* 1.3 77.3 - - - +
334A ALA* 1.3 55.6 + - - +
336A ILE* 4.6 0.4 - - - -
337A ALA* 2.8 27.5 + - - +
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Residues in contact with ALA 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A MET* 4.0 12.2 - - + +
295A ARG* 4.9 2.4 + - - -
299A PRO* 5.7 0.7 - - - -
330A ARG 2.9 16.5 + - - +
331A GLN* 3.6 9.0 - - - +
333A ALA* 1.3 76.0 - - - +
335A GLN* 1.3 62.3 + - + +
337A ALA* 3.5 7.1 + - - +
338A ASP* 3.2 21.1 + - - +
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Residues in contact with GLN 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLN* 3.0 28.6 + - - +
332A THR* 3.6 12.9 + - + +
334A ALA* 1.3 75.3 - - + +
336A ILE* 1.3 67.9 + - + +
338A ASP* 3.2 7.1 + - - +
339A TYR* 3.0 22.5 + - - +
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Residues in contact with ILE 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PRO* 5.6 2.9 - - + +
260A LEU* 4.0 26.2 - - + -
272A PRO* 4.0 14.1 - - + -
332A THR* 2.9 34.4 + - + +
333A ALA* 3.9 3.1 - - - +
335A GLN* 1.3 73.9 - - + +
337A ALA* 1.3 67.3 + - - +
339A TYR* 3.3 16.2 + - + +
340A ILE* 2.9 27.3 + - + +
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A TRP* 3.8 26.5 - - + -
272A PRO* 3.8 11.6 - - + +
295A ARG* 4.5 9.2 - - - -
299A PRO* 4.4 12.1 - - + -
333A ALA 2.8 18.9 + - - +
334A ALA* 3.6 8.5 - - - +
335A GLN 3.3 0.2 - - - -
336A ILE* 1.3 77.1 - - - +
338A ASP* 1.3 62.2 + - - +
340A ILE* 3.6 1.1 - - - +
341A ARG* 3.1 31.6 + - - +
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Residues in contact with ASP 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ARG* 2.9 37.4 + - - +
334A ALA 3.2 12.1 + - - +
335A GLN* 3.2 10.0 + - - +
337A ALA* 1.3 76.4 - - - +
339A TYR* 1.3 65.4 + - - +
341A ARG* 3.5 7.1 + - - +
342A ARG* 3.6 26.0 + - - +
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Residues in contact with TYR 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLN 3.0 13.4 + - - +
336A ILE* 3.3 22.6 + - + +
338A ASP* 1.3 77.6 + - - +
340A ILE* 1.3 83.6 + - + +
342A ARG* 3.2 25.3 + - - +
343A MET* 4.3 14.9 + - + +
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Residues in contact with ILE 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 4.1 28.0 - - + -
264A TRP* 3.8 23.1 - - + -
270A ALA* 3.6 19.7 - - + +
272A PRO* 4.7 4.5 - - + -
336A ILE* 2.9 22.1 + - + +
337A ALA* 3.6 7.0 - - - +
339A TYR* 1.3 92.8 - - + +
341A ARG* 1.3 65.2 + - - +
343A MET* 3.0 34.5 + - - +
348A PRO* 5.1 2.7 - - + +
349A HIS* 3.6 30.2 - - + +
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Residues in contact with ARG 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A TRP* 3.5 17.3 - - + -
269A HIS* 5.1 0.2 + - - -
295A ARG* 3.8 25.6 - - - +
296A PHE* 3.3 59.4 - - - -
337A ALA 3.1 24.7 + - - +
338A ASP 3.9 2.5 - - - +
339A TYR 3.2 0.2 - - - -
340A ILE* 1.3 77.0 - - - +
342A ARG* 1.3 60.6 + - - +
343A MET 3.0 0.4 - - - -
344A GLY* 3.1 32.8 + - - -
349A HIS* 3.0 26.5 + - - -
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Residues in contact with ARG 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ASP* 3.6 26.4 + - - +
339A TYR* 3.5 15.0 - - - +
340A ILE 3.1 1.6 - - - -
341A ARG* 1.3 76.8 - - + +
343A MET* 1.3 58.5 + - - +
344A GLY* 3.3 1.0 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il